Thanks for suck a great plugin! Its really smart idea to avoid using some multilingual plugins that will conflict with other one and use originally build in wordpress multisite system. Based on it multilingual site is more clear and bug free!!!
I wounder, when this feature will appear to link custom post types and their categories.

Now that custom post types are supported (works great as far as I can see), the only missing feature is support for custom taxonomies. Right now the extra column is added, but the flag icons link to a post edit page instead of a tag/category edit page.

Let me grab the chance to thank you as well, this is a really useful plugin.
Regarding CPTs, is there a way to link them on a parent level similarly to post categories linking?
I'm not referring to taxonomies (lets say 'actors') but at the CPTs' base ('movies').

Well, at the moment you can link individual CPT posts for example lets say we have a specific movie called "Immortals", linking from one language to another is no problem.
You can also link their taxonomies (e.g. actors, director etc) so when one is overlooking the actors archive they get transfered from one language to another - again no problem.

But, if am not mistaken, I don't see a way to link their base (e.g. movies). So that when one is overlooking the movies archive, the language switch would transfer the visitor on the movies archive of the other language(s).

The assumption being that the word "movies" was used as the $post_type parameter in the register_post_type( $post_type, $args ) function.